My experience with e-standby upgrades when using certificates is this...

When using a suite/room upgrade, the e-standby proposals are based on the original room booked as the starting point, and not the room you're upgrading into. So, the proposals may not be that great. I've seen them offer me the chance to pay an additional amount to get a room worse than the one I was already confirmed in through my upgrade cert!

I went so far as to test this out with duplicate reservations. After I had a confirmed reservation with my certs applied, I booked a second reservation for the higher level room that I had the upgrade confirmed into. Then compared the e-standby offers, and the additional amounts they were looking for to upgrade into the best rooms were less than the offers through my first reservation with the upgrade applied.

When using free night certs on a reservation, when you accept an e-standby upgrade, the additional nightly upgrade rate offered will be charged for each night of the stay, including the free nights.

Sometimes it's still a good deal, but sometimes it's not.